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Associative transcriptomics of traits in the polyploid crop species Brassica napus

Abstract

Association genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. But most crops are polyploid, making it difficult to identify the required markers and to assemble a genome sequence to order those markers. To circumvent this difficulty, we developed associative transcriptomics, which uses transcriptome sequencing to identify and score molecular markers representing variation in both gene sequences and gene expression, and correlate this with trait variation. Applying the method in the recently formed tetraploid crop Brassica napus, we identified genomic deletions that underlie two quantitative trait loci for glucosinolate content of seeds. The deleted regions contained orthologs of the transcription factor HAG1 (At5g61420), which controls aliphatic glucosinolate biosynthesis in Arabidopsis thaliana. This approach facilitates the application of association genetics in a broad range of crops, even those with complex genomes.

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Figure 1: Collinearity of chromosome C2 with the genome of A. thaliana.
Figure 2: Distribution of mapped markers associating with the erucic acid trait.
Figure 3: The identification of sequence variation–based (SNP) and expression variation–based (GEM) markers providing the transcription factor HAG1 gene family as a candidate in the quantitative control of glucosinolate content of rapeseed.

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Sequence Read Archive

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Acknowledgements

We thank The Genome Analysis Centre for generating Illumina sequence data. This work was supported by UK Biotechnology and Biological Sciences Research Council (BBSRC BB/H004351/1 (IBTI Club), BB/E017363/1, ERAPG08.008) and UK Department for Environment, Food and Rural Affairs (Defra IF0144). We would like to thank R. Snowdon, J. Barker and G. Teakle for providing germplasm. We would like to thank D. Manning and M. Turner of KWS-UK and P. Tillmann of Verband Deutscher Landwirtschaftlicher Untersuchungs und Forschungsanstalten (VDLUFA) Qualitatssicherung NIRS/NIT, Kassel, Germany, for their assistance with NIRS measurements.

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Authors and Affiliations

Authors

Contributions

I.B. and A.L.H. conceived and planned the project. A.L.H., F.F., R.W., L.C. and C.H. carried out the experiments. I.B., A.L.H., M.T., J.H. and F.F. performed data analysis. P.W. provided materials and field data. I.B. and A.L.H. wrote the manuscript and all authors reviewed it.

Corresponding author

Correspondence to Ian Bancroft.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 (PDF 11057 kb)

Supplementary Table 1

B. rapa and B. oleracea genome scaffolds forming the B. napus pseudomolecules (XLSX 93 kb)

Supplementary Table 2

Coordinates for splitting of Brassica rapa and Brassica oleracea genome assembly scaffolds (XLSX 14 kb)

Supplementary Table 3

Unigene-based map of the Brassica napus genome (XLSX 9050 kb)

Supplementary Table 4

Brassica napus accessions (XLSX 11 kb)

Supplementary Table 5

mRNAseq coverage data (XLSX 16 kb)

Supplementary Table 6

GWAS data matrix for 84 Brassica napus accessions (XLSX 22226 kb)

Supplementary Table 7

NIRS data for 53 accessions (XLSX 13 kb)

Supplementary Table 8

Structure Q matrix for K=2 populations (XLSX 12 kb)

Supplementary Table 9

WGCNA analysis (XLSX 39 kb)

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Harper, A., Trick, M., Higgins, J. et al. Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 30, 798–802 (2012). https://doi.org/10.1038/nbt.2302

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